GLOBAL MAPPING OF SMALL RNA-TARGET INTERACTIONS IN BACTERIA

Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq were acknowledged as major posttranscriptional regulators in bacteria. Deciphering the sRNA-target interactome is an essential step towards understanding the roles of sRNAs in the cellular networks. Here we developed a methodology termed RIL-seq (RNA Interaction by Ligation and sequencing), which integrates experimental and computational tools for in-vivo transcriptome-wide identification of sRNA-target pairs associated with Hfq. Application of this methodology to Escherichia coli has allowed us to snapshot its posttranscriptional regulatory network under various conditions, revealing changes in the repertoire of Hfq-bound sRNAs as well as re-wiring of the network between conditions. We expand the repertoire of targets for known sRNAs, discover putative novel Hfq-bound sRNAs encoded in 3`UTR, 5`UTR, CDS, intergenic-regions and antisense of genes along with their trans targets, and provide insights into the binding of sRNAs and mRNAs within Hfq.